Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.7 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2012 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.7-exp dom mar 10 23:17:04 UTC 2013 ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> W E L C O M E to PDBStat <================ PDBStat has become a tool able (between other things) of: a) read and interconvert between DISMAN, DYANA, PDB, DISCOVER, IMPACT b) elaborate some info about the molecule as MW, Radius of gyration, .. c) investigate the setereochemical quality of a protein by evaluating phi, psi, chi1, impropers and chirality The sequence of acts should be: 1.- read a file (coords, constr) 2.- read a sequence file (can be free format) 3.- Follow menu (calculating, writing ...) NOTE: Be aware that if you read in a constraint file you *ALWAYS* need to read a sequence file also HAVE FUN AND ENJOY !! **** For more info type `help' or `menu' **** --> ... Reading/Loading Distances file ... 125 distance records read --> ... Reading/Loading Dihedral Library .. 1119 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `HR3102A_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 86 MET GLY HIS HIS HIS HIS HIS HIS SER HIS PRO ASN GLU 1 > ReadCoordsPdb(): Counting models in file `HR3102A_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file HR3102A_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 27280 ATOM records read from file > ReadCoordsPdb(): --> 27280 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > calc_order_parameters(): ... Evaluating Dihedrals CHAIN .GT. SUM.GT. RES ID DIH S(phi) S(psi) S(chi1) S(chi2) S(chi3) S(chi4) S(chi5) 0.90 1.6 ----------------------------------------------------------------------------------- MET A 1 0.327 0.712 0.511 0.208 GLY A 2 0.209 0.299 HIS A 3 0.762 0.495 0.489 0.469 HIS A 4 0.825 0.720 0.657 0.684 HIS A 5 0.885 0.474 0.465 0.462 HIS A 6 0.690 0.389 0.553 0.429 HIS A 7 0.791 0.648 0.538 0.373 HIS A 8 0.817 0.626 0.702 0.618 SER A 9 0.769 0.272 0.564 HIS A 10 0.308 0.801 0.474 0.202 PRO A 11 0.990 0.980 0.925 0.870 11 11 ASN A 12 0.989 0.980 0.230 0.935 12 12 GLU A 13 0.999 1.000 1.000 1.000 0.983 13 13 GLU A 14 1.000 0.999 1.000 0.582 0.929 14 14 ALA A 15 1.000 0.999 15 15 ARG A 16 0.999 0.999 0.875 0.996 0.292 0.769 1.000 16 16 LEU A 17 1.000 1.000 1.000 1.000 17 17 ASP A 18 1.000 1.000 1.000 1.000 18 18 ILE A 19 1.000 1.000 1.000 1.000 19 19 LEU A 20 1.000 1.000 0.999 0.999 20 20 LYS A 21 1.000 1.000 1.000 1.000 0.998 0.997 21 21 ILE A 22 1.000 1.000 1.000 1.000 22 22 HIS A 23 1.000 0.999 0.999 0.996 23 23 SER A 24 0.999 0.997 1.000 24 24 ARG A 25 0.989 0.983 0.688 0.999 0.930 0.881 1.000 25 25 LYS A 26 0.984 0.985 0.999 0.854 1.000 0.998 26 26 MET A 27 0.966 0.992 0.842 0.992 0.483 27 27 ASN A 28 0.991 0.970 0.877 0.943 28 28 LEU A 29 0.974 0.995 0.999 1.000 29 29 THR A 30 0.993 0.973 0.999 30 30 ARG A 31 0.982 0.407 0.678 1.000 0.745 0.997 1.000 GLY A 32 0.339 0.924 ILE A 33 0.923 0.979 0.999 1.000 33 33 ASN A 34 0.968 0.998 0.999 0.990 34 34 LEU A 35 0.995 0.996 1.000 1.000 35 35 ARG A 36 1.000 1.000 0.999 0.935 0.670 0.709 1.000 36 36 LYS A 37 1.000 1.000 0.996 0.980 0.879 0.914 37 37 ILE A 38 1.000 1.000 0.999 0.999 38 38 ALA A 39 1.000 1.000 39 39 GLU A 40 1.000 1.000 1.000 0.919 0.979 40 40 LEU A 41 0.998 0.993 1.000 1.000 41 41 MET A 42 0.988 0.986 0.850 0.699 0.261 42 42 PRO A 43 0.996 0.430 0.969 0.940 GLY A 44 0.419 0.820 ALA A 45 0.814 0.989 45 SER A 46 0.964 0.981 0.769 46 46 GLY A 47 1.000 0.999 47 47 ALA A 48 1.000 1.000 48 48 GLU A 49 0.997 0.999 0.998 0.680 0.764 49 49 VAL A 50 1.000 1.000 1.000 50 50 LYS A 51 1.000 1.000 1.000 1.000 1.000 1.000 51 51 GLY A 52 1.000 1.000 52 52 VAL A 53 1.000 1.000 1.000 53 53 CYS A 54 1.000 1.000 1.000 54 54 THR A 55 1.000 1.000 1.000 55 55 GLU A 56 1.000 1.000 1.000 0.997 0.975 56 56 ALA A 57 1.000 1.000 57 57 GLY A 58 1.000 1.000 58 58 MET A 59 1.000 1.000 1.000 1.000 1.000 59 59 TYR A 60 1.000 1.000 0.987 0.506 60 60 ALA A 61 1.000 1.000 61 61 LEU A 62 1.000 0.999 1.000 1.000 62 62 ARG A 63 1.000 1.000 1.000 0.999 0.634 0.992 1.000 63 63 GLU A 64 1.000 1.000 0.999 0.999 0.913 64 64 ARG A 65 0.999 0.997 1.000 1.000 1.000 1.000 1.000 65 65 ARG A 66 0.975 0.992 0.998 0.999 0.736 0.459 1.000 66 66 VAL A 67 0.999 0.998 1.000 67 67 HIS A 68 0.983 0.987 1.000 0.998 68 68 VAL A 69 0.991 0.998 1.000 69 69 THR A 70 0.999 0.999 1.000 70 70 GLN A 71 1.000 1.000 1.000 0.946 0.913 71 71 GLU A 72 1.000 1.000 0.582 0.998 0.915 72 72 ASP A 73 1.000 1.000 0.999 0.601 73 73 PHE A 74 1.000 0.999 0.999 0.899 74 74 GLU A 75 1.000 0.999 0.763 0.997 0.856 75 75 MET A 76 1.000 1.000 1.000 1.000 1.000 76 76 ALA A 77 1.000 1.000 77 77 VAL A 78 1.000 1.000 1.000 78 78 ALA A 79 1.000 0.999 79 79 LYS A 80 0.999 1.000 1.000 0.999 0.999 0.999 80 80 VAL A 81 0.995 0.998 1.000 81 81 MET A 82 0.998 0.980 1.000 0.999 1.000 82 82 GLN A 83 0.998 0.983 0.999 0.766 0.867 83 83 LYS A 84 0.855 0.757 0.453 0.480 0.999 0.926 ASP A 85 0.535 0.375 0.435 0.903 SER A 86 0.712 1.000 Ranges: 3 from: A 11 to A 30 from: A 33 to A 42 from: A 46 to A 83 PdbStat> > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone onto model 1 > do_average_coords(): Calc. average coordinates backbone > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 1 is: 0.390 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 2 is: 0.375 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 3 is: 0.446 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 4 is: 0.486 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 5 is: 0.257 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 6 is: 0.380 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 7 is: 0.371 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 8 is: 0.429 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 9 is: 0.364 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 10 is: 0.454 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 11 is: 0.427 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 12 is: 0.324 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 13 is: 0.351 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 14 is: 0.246 (*) > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 15 is: 0.384 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 16 is: 0.307 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 17 is: 0.428 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 18 is: 0.468 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 19 is: 0.410 > Kabsch RMSD of backbone atoms in res. A[11..30],A[33..42],A[46..83],for model 20 is: 0.496 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..30],[33..42],[46..83], is: 0.390 > Range of RMSD values to reference struct. is 0.246 to 0.496 > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 1 is: 0.701 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 2 is: 0.649 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 3 is: 0.829 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 4 is: 0.721 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 5 is: 0.506 (*) > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 6 is: 0.618 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 7 is: 0.532 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 8 is: 0.797 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 9 is: 0.695 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 10 is: 0.652 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 11 is: 0.685 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 12 is: 0.593 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 13 is: 0.647 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 14 is: 0.593 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 15 is: 0.612 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 16 is: 0.595 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 17 is: 0.644 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 18 is: 0.666 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 19 is: 0.784 > Kabsch RMSD of heavy atoms in res. A[11..30],A[33..42],A[46..83],for model 20 is: 0.716 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..30],[33..42],[46..83], is: 0.662 > Range of RMSD values to reference struct. is 0.506 to 0.829 PdbStat> PdbStat> *END* of program detected, BYE! ...